[R-pkgs] New Quantian release with over 800 CRAN/BioC packages

[ Reposting this here as this Quantian release contains
- all CRAN packages as of December 10, 2005
* except the Windows only ones (BRugs, mimR, rcom, RWinEdt)
* and three that would not build (Rlsf, ROracle, rJava) for lack of
Java, Oracle or rlsf
- all BioC packages for release 1.8
* excecpt RMAGEML (needs Java)
- for a total of over 800 R packages
- a couple other R niceties: (X)Emacs + ESS, Ggobi, Rpad, RKward...)
I hope this isn't considered off-topic here; if so please let me know
in private mail and I will refrain from posting in the future. -- Dirk ]
(Please see note [1] below regarding recipients for this posting. Thanks!)
Executive Summary:
Quantian 0.7.9.1 is the first Quantian release based on Knoppix 4.0.2.
Quantian adds hundreds of scientific / numeric packages, as well as the
openMosix enabled 2.4.27 kernel, to the cdrom version of Knoppix.
Relative to the previous release 0.6.9.3, hundreds of applications have
been updated, and many new applications (such as polyxmass, scigraphica,
kst, octaviz, gromacs) have been added. Quantian now contains over 2400
Debian packages, and over 800 packages for R.
Quantian comes as one bootable dvd iso of 2.5gb (compressed) with
almost 7 gb (uncompressed) of software of interest to quantitative
analysts, scientists, researchers or students.
Announcing Quantian release 0.7.9.1
===================================
I What is it?
Quantian is a remastering of Knoppix, the self-configuring and directly
bootable cdrom/dvd that turns any pc or laptop into a full-featured Linux
workstation, and (parts of) clusterKnoppix, which adds support for
openMosix-based cluster computing. However, Quantian differs from
Knoppix by having a particular focus on quantitative, numerical or
scientific applications, and hence adds a very large set of programs of
interest to applied or theoretical workers in quantitative or data-driven
fields to the solid base provided by Knoppix.
See http://dirk.eddelbuettel.com/quantian.html for more details.
II What Quantian highlights should I care about ?
o First release based on Knoppix 4.0.2: Derived from the cdrom version of
Knoppix, Quantian utilises the unionfs setup of Knoppix to combine two
compressed loop images for a total of 2.5 gb (from two files of 2.0 gb
and 425 mb) corresponding to almost 7 gb of software.
o KDE 3.4, Kernel 2.6.12; added backport of kernel 2.4.27 with openMosix
patch for continued openMosix support [ but note that openMosix and
unionfs seem to conflict so kernel 2.4.27 only sees the first
compressed loop image ]
o Some highlights in 0.7.9.1 are
- very complete R support with over 800 packages (28 from 'core R',
another 70 from Debian packages, and 724 directly installed from
CRAN and BioConductor, covering over 99% of all packages at CRAN
and BioConductor [ not counting a handful of windows-only CRAN
packages ] ), ESS editing in Emacs/XEmacs, GGobi visualization,
Rpad webinterface, and initial support for the RKward GUI;
- even stronger bioinformatics/biology support than before:
BioConductor, arb, biofox, bioperl, biopython, blast2, boxshade,
bugsx, clustalw, fastdnaml, fastlink, garlic, gromacs, hmmer, loki,
mipe, molphy, muscle, ncbi, phylip, rasmol, readseq, seaview,
t-coffee, textopo, and more;
- continued strong mathematics / computational algrebra support: axiom,
blacs, calc, euler, gap, giac, mathomatic, maxima, pari, scalapack,
scilab, texmacs, yacas, yorick;
- strong visualization / graphics support: dx, garlic, gdpc, gnuplot,
grace, grass, gri, illuminator, kst, labplot, mayavi, matplot, proj,
plplot, plotmtv, rasmol, starplot, vtk, xd3d, xgraph, ygraph;
- large number of programming and scripting languages, editors,
debuggers and libraries;
- excellent latex support with auctex, lyx, kile, texmacs interface,
as well as numerous macro packages, bibtex tools;
- office support via openoffice and koffice suites, abiword, gnumeric
and other applications;
- plus all the tools and toys from the current Knoppix relase.
o See http://dirk.eddelbuettel.com/quantian/changelog.html for details.
o See http://dirk.eddelbuettel.com/quantian/howto.html for several
short HOWTOs on booting Quantian from hd on either Windows or Linux,
booting via a bootcd (such as clusterKnoppix), or botting from a
USB memory device. Contributions, corrections, and feedback on these
HOWTOs is always appreciated.
III Where do I get it?
o Downloads are available from the main host at Seattle at FHCRC:
http://quantian.fhcrc.org/rsync://quantian.fhcrc.org/quantian/
and at the East Coast at
http://research.warnes.net/downloads/quantian/CURRENT/ftp://research.warnes.net/users/edd/quantian/CURRENT/
The most recent release is also available at
http://quantian.alioth.debian.org/
Note that file size of 2.5 gb may upset web caching system such
as squid. It may be best to rely on rsync or bittorrent instead
of http.
o Bittorrents should be available shortly at
http://www.tlm-project.org/public/distributions/quantian/
o The main European mirrors should catch up shortly:
http://sunsite.rediris.es/mirror/quantianhttp://sunsite.informatik.rwth-aachen.de/ftp/pub/Linux/quantian
o CD/DVD vendors will probably update their offerings soon as well.
See the Quantian site for a list.
IV Mailing lists
o Two mailing lists exist for Quantian
quantian-announce for announcements, intended to be low volume
quantian-general for general discussions about Quantian
available via
http://alioth.debian.org/mail/?group_id=30303
for subscription info etc., and start using the quantian-general lists
for general questions, comments, suggestions or discussions about
Quantian.
Quantian-general is subscribed to quantian-announce, so you only need
to subscribe to one (but can of course subscribe to both). Posting to
quantian-general requires a subscription.
Reply-To: for this message is quantian-general at lists.alioth.debian.org
so that discussions can be continued on the list.
V Known Bugs in 0.7.9.1
o Debian's current C++ transition affects the KDE packages. Several
packages had to be installed from the stable relase, and a few
(celestia, gdal) are currently uninstallable. This should should
improve over the next few weeks/months.
o Kdvi is broken. However, xdvi works as do the various pdf previewers
so (PDF)LaTeX use is still possible.
o As noticed above, when openMosix and kernel 2.4.27 are used, the
second compressed loop image is not accessible implying that the
/opt, /usr/games, /usr/lib/j2se, /usr/share/doc, /usr/src, /usr/NX
directories are not accessible.
VI Other items
o Feedback / poll on package additions or removal
As always, I welcome comments and suggestions about programs to be
added or removed. Existing Debian packages, and possibly existing
rpm packages, typically get inserted quite readily.
Please send feedback, questions, comments, ... to the
quantian-general at lists.alioth.debian.org
list to maximise the number of eyes glancing at any one question.
Notice that a subscription to the list is needed in order to post.
o Feedback would also be appreciated on ways to better communicate with
difference scientific communities that could be interested in Quantian.
VII Notes
[1] This email is sent via the quantian-announce mailing list. I have
subscribed those whose email addresses are in my quantian mail folder
due to prior emails. The quantian-announce mailing list only sends
moderator-approved posts -- so there should be no spam whatsoever.
Anybody who considers this unwanted is kindly asked to send me a
private mail to get unsubscribed immediately. Otherwise, replies and
follow-ups should go to
quantian-general at lists.alioth.debian.org
where posting may require an initial subscription.
Best regards, Dirk
--
Hell, there are no rules here - we're trying to accomplish something.
-- Thomas A. Edison